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This page was generated on 2024-07-03 10:19 -0400 (Wed, 03 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4480
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4511
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4469
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1138/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Maaslin2 1.18.0  (landing page)
Lauren McIver
Snapshot Date: 2024-06-30 14:00 -0400 (Sun, 30 Jun 2024)
git_url: https://git.bioconductor.org/packages/Maaslin2
git_branch: RELEASE_3_19
git_last_commit: 35350f9
git_last_commit_date: 2024-04-30 11:16:06 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Maaslin2 on nebbiolo1

To the developers/maintainers of the Maaslin2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Maaslin2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Maaslin2
Version: 1.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
StartedAt: 2024-07-01 00:38:45 -0400 (Mon, 01 Jul 2024)
EndedAt: 2024-07-01 00:42:49 -0400 (Mon, 01 Jul 2024)
EllapsedTime: 244.6 seconds
RetCode: 0
Status:   OK  
CheckDir: Maaslin2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 86.813  1.132  87.892
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

Installation output

Maaslin2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.11
Current TMB version is 1.9.13
Please re-install glmmTMB from source or restore original ‘TMB’ package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

Tests output

Maaslin2.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-07-01 00:40:42.845813 INFO::Writing function arguments to log file
2024-07-01 00:40:42.888781 INFO::Verifying options selected are valid
2024-07-01 00:40:42.927609 INFO::Determining format of input files
2024-07-01 00:40:42.929181 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-01 00:40:42.934208 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-01 00:40:42.935593 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-07-01 00:40:42.938154 INFO::Filter data based on min abundance and min prevalence
2024-07-01 00:40:42.939153 INFO::Total samples in data: 1595
2024-07-01 00:40:42.93997 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-01 00:40:42.943714 INFO::Total filtered features: 0
2024-07-01 00:40:42.944708 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-01 00:40:42.958846 INFO::Total filtered features with variance filtering: 0
2024-07-01 00:40:42.959929 INFO::Filtered feature names from variance filtering:
2024-07-01 00:40:42.96078 INFO::Running selected normalization method: TSS
2024-07-01 00:40:44.172345 INFO::Bypass z-score application to metadata
2024-07-01 00:40:44.173679 INFO::Running selected transform method: AST
2024-07-01 00:40:44.189565 INFO::Running selected analysis method: LM
2024-07-01 00:40:44.672833 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-01 00:40:45.037246 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-01 00:40:45.195927 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-01 00:40:45.34355 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-01 00:40:45.497024 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-01 00:40:45.637578 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-01 00:40:45.777065 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-01 00:40:45.916839 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-01 00:40:46.031344 WARNING::Fitting problem for feature 8 a warning was issued
2024-07-01 00:40:46.174445 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-01 00:40:46.281589 WARNING::Fitting problem for feature 9 a warning was issued
2024-07-01 00:40:46.436404 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-01 00:40:46.571045 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-01 00:40:46.708508 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-01 00:40:46.872552 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-01 00:40:46.992487 WARNING::Fitting problem for feature 13 a warning was issued
2024-07-01 00:40:47.141031 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-01 00:40:47.280767 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-01 00:40:47.432571 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-01 00:40:47.568641 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-01 00:40:47.71057 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-01 00:40:47.879587 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-01 00:40:48.023921 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-01 00:40:48.167507 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-01 00:40:48.328275 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-01 00:40:48.467703 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-01 00:40:48.603851 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-01 00:40:48.746331 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-01 00:40:48.89683 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-01 00:40:49.038921 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-01 00:40:49.190904 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-01 00:40:49.345113 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-01 00:40:49.492565 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-01 00:40:49.630917 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-01 00:40:49.782221 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-01 00:40:49.928517 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-01 00:40:50.081752 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-01 00:40:50.22832 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-01 00:40:50.369353 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-01 00:40:50.510217 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-01 00:40:50.665591 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-01 00:40:50.801718 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-01 00:40:50.941823 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-01 00:40:51.085334 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-01 00:40:51.225518 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-01 00:40:51.376208 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-01 00:40:51.514288 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-01 00:40:51.652808 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-01 00:40:51.791248 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-01 00:40:51.931934 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-01 00:40:52.080169 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-01 00:40:52.216845 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-01 00:40:52.36267 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-01 00:40:52.498745 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-01 00:40:52.668381 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-01 00:40:52.818885 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-01 00:40:52.980089 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-01 00:40:53.118653 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-01 00:40:53.27582 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-01 00:40:53.432543 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-01 00:40:53.589452 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-01 00:40:53.735281 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-01 00:40:53.87829 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-01 00:40:54.02065 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-01 00:40:54.158737 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-01 00:40:54.302459 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-01 00:40:54.47479 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-01 00:40:54.616145 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-01 00:40:54.75662 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-01 00:40:54.899243 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-01 00:40:55.043417 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-01 00:40:55.18919 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-01 00:40:55.351902 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-01 00:40:55.511896 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-01 00:40:55.647822 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-01 00:40:55.786495 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-01 00:40:55.932468 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-01 00:40:56.073046 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-01 00:40:56.213953 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-01 00:40:56.360753 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-01 00:40:56.500576 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-01 00:40:56.647292 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-01 00:40:56.798395 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-01 00:40:56.935519 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-01 00:40:57.079199 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-01 00:40:57.227749 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-01 00:40:57.365583 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-01 00:40:57.507907 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-01 00:40:57.6466 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-01 00:40:57.787187 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-01 00:40:57.974481 INFO::Counting total values for each feature
2024-07-01 00:40:58.007117 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-07-01 00:40:58.152876 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-07-01 00:40:58.305136 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-07-01 00:40:58.457104 INFO::Writing residuals to file output/fits/residuals.rds
2024-07-01 00:40:58.515115 INFO::Writing fitted values to file output/fits/fitted.rds
2024-07-01 00:40:58.548174 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-07-01 00:40:58.830765 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-07-01 00:40:58.838092 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-07-01 00:40:58.850713 INFO::Writing function arguments to log file
2024-07-01 00:40:58.856431 INFO::Verifying options selected are valid
2024-07-01 00:40:58.857384 INFO::Determining format of input files
2024-07-01 00:40:58.858442 INFO::Input format is data samples as rows and metadata samples as rows
2024-07-01 00:40:58.862945 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-07-01 00:40:58.863936 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-07-01 00:40:58.865468 INFO::Filter data based on min abundance and min prevalence
2024-07-01 00:40:58.866294 INFO::Total samples in data: 1595
2024-07-01 00:40:58.867142 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-07-01 00:40:58.870858 INFO::Total filtered features: 0
2024-07-01 00:40:58.871771 INFO::Filtered feature names from abundance and prevalence filtering:
2024-07-01 00:40:58.878347 INFO::Total filtered features with variance filtering: 0
2024-07-01 00:40:58.87937 INFO::Filtered feature names from variance filtering:
2024-07-01 00:40:58.88018 INFO::Running selected normalization method: NONE
2024-07-01 00:40:58.880983 INFO::Bypass z-score application to metadata
2024-07-01 00:40:58.881765 INFO::Running selected transform method: AST
2024-07-01 00:40:58.89496 INFO::Running selected analysis method: LM
2024-07-01 00:40:58.896456 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-07-01 00:40:59.026815 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-07-01 00:40:59.16709 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-07-01 00:40:59.295824 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-07-01 00:40:59.428341 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-07-01 00:40:59.556472 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-07-01 00:40:59.6978 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-07-01 00:40:59.829566 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-07-01 00:40:59.964202 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-07-01 00:41:00.104466 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-07-01 00:41:00.239948 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-07-01 00:41:00.350079 WARNING::Fitting problem for feature 11 a warning was issued
2024-07-01 00:41:00.489118 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-07-01 00:41:00.623394 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-07-01 00:41:00.755818 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-07-01 00:41:00.884428 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-07-01 00:41:01.023201 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-07-01 00:41:01.127414 WARNING::Fitting problem for feature 16 a warning was issued
2024-07-01 00:41:01.258309 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-07-01 00:41:01.397389 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-07-01 00:41:01.527977 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-07-01 00:41:01.655192 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-07-01 00:41:01.797826 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-07-01 00:41:01.930696 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-07-01 00:41:02.07005 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-07-01 00:41:02.207903 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-07-01 00:41:02.342594 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-07-01 00:41:02.475046 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-07-01 00:41:02.61108 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-07-01 00:41:02.743928 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-07-01 00:41:03.082206 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-07-01 00:41:03.207657 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-07-01 00:41:03.337382 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-07-01 00:41:03.475307 INFO::Fitting model to feature number 32, Prevotella.copri
2024-07-01 00:41:03.617195 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-07-01 00:41:03.744808 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-07-01 00:41:03.874812 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-07-01 00:41:04.003181 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-07-01 00:41:04.140421 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-07-01 00:41:04.272828 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-07-01 00:41:04.404863 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-07-01 00:41:04.536804 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-07-01 00:41:04.661737 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-07-01 00:41:04.791615 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-07-01 00:41:04.920396 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-07-01 00:41:05.295307 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-07-01 00:41:05.433908 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-07-01 00:41:05.569736 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-07-01 00:41:05.712108 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-07-01 00:41:05.850258 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-07-01 00:41:05.987494 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-07-01 00:41:06.120314 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-07-01 00:41:06.256896 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-07-01 00:41:06.413179 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-07-01 00:41:06.549618 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-07-01 00:41:06.684998 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-07-01 00:41:06.832832 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-07-01 00:41:06.964372 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-07-01 00:41:07.096742 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-07-01 00:41:07.238531 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-07-01 00:41:07.367232 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-07-01 00:41:07.499537 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-07-01 00:41:07.630302 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-07-01 00:41:07.757026 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-07-01 00:41:07.884195 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-07-01 00:41:08.018397 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-07-01 00:41:08.147687 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-07-01 00:41:08.278111 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-07-01 00:41:08.404147 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-07-01 00:41:08.518502 WARNING::Fitting problem for feature 67 a warning was issued
2024-07-01 00:41:08.656719 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-07-01 00:41:08.782746 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-07-01 00:41:08.921144 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-07-01 00:41:09.057726 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-07-01 00:41:09.191381 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-07-01 00:41:09.23695 WARNING::Fitting problem for feature 72 a warning was issued
2024-07-01 00:41:09.370213 INFO::Fitting model to feature number 73, Dialister.invisus
2024-07-01 00:41:09.502424 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-07-01 00:41:09.640142 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-07-01 00:41:09.771549 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-07-01 00:41:09.913747 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-07-01 00:41:10.043263 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-07-01 00:41:10.174392 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-07-01 00:41:10.31496 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-07-01 00:41:10.442452 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-07-01 00:41:10.581925 INFO::Fitting model to feature number 82, Escherichia.coli
2024-07-01 00:41:10.708942 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-07-01 00:41:10.841533 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-07-01 00:41:10.976358 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-07-01 00:41:11.383954 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-07-01 00:41:11.52088 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-07-01 00:41:11.675392 INFO::Counting total values for each feature
2024-07-01 00:41:11.698272 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-07-01 00:41:11.842675 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-07-01 00:41:11.989612 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-07-01 00:41:12.143525 INFO::Writing residuals to file output2/fits/residuals.rds
2024-07-01 00:41:12.218889 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-07-01 00:41:12.291795 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-07-01 00:41:12.29772 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-07-01 00:41:12.303163 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 30.111   0.548  30.648

Example timings

Maaslin2.Rcheck/Maaslin2-Ex.timings

nameusersystemelapsed
Maaslin286.813 1.13287.892